The thing about Barnabas is that despite everything that happens in 1840/41, Barnabas does somehow still exist in the present because Liz recognizes him in Ep #1198. In fact, very strangely, Liz acts as if Barn, Julia and Stokes had never been gone. Try explaining that away.
Though, actually, someone has tried - for The Dark Shadows Concordance 1840, Arthur Warren Oddsson wrote a lengthy (something like 15 page) essay that attempts to reconcile all the supposed inconsistencies. It's much too complicated to try to summarize here, and I'm not sure I agree with all of his theories (though his theories that somehow the I Ching and the Stairway Through Time played parts in correcting Barnabas' existence do make sense), but the essay is an absolutely fascinating read, and it's most defintely something worth checking out if you never have.